[English] 日本語
Yorodumi
- EMDB-51916: Structure of the outer membrane exopolysaccharide transporter PelBC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51916
TitleStructure of the outer membrane exopolysaccharide transporter PelBC
Map data
Sample
  • Complex: Exopolysaccharide transporter PelBC
    • Protein or peptide: PelB
    • Protein or peptide: PelC
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsExopolysaccharide / Complex / Acyl-chain / TRANSPORT PROTEIN
Function / homology
Function and homology information


polysaccharide transport / single-species biofilm formation / membrane
Similarity search - Function
: / PelB, C-terminal beta barrel domain / Tetratricopeptide repeat / : / Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBenedens M / Rosales C / Beckmann R / Kedrov A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas aeruginosa.
Authors: Marius Benedens / Cristian Rosales-Hernandez / Sabine A P Straathof / Jennifer Loschwitz / Otto Berninghausen / Giovanni Maglia / Roland Beckmann / Alexej Kedrov /
Abstract: The pathogen Pseudomonas aeruginosa enhances its virulence and antibiotic resistance upon formation of durable biofilms. The exopolysaccharides Pel, Psl and alginate essentially contribute to the ...The pathogen Pseudomonas aeruginosa enhances its virulence and antibiotic resistance upon formation of durable biofilms. The exopolysaccharides Pel, Psl and alginate essentially contribute to the biofilm matrix, but their secretion mechanisms are barely understood. Here, we reveal the architecture of the outer membrane complex PelBC for Pel export, where the essential periplasmic ring of twelve lipoproteins PelC is mounted on top of the nanodisc-embedded β-barrel PelB. The PelC assembly is stabilized by electrostatic contacts with the periplasmic rim of PelB and via the membrane-anchored acyl chains. The negatively charged interior of the PelB β-barrel forms a route for the cationic Pel exopolysaccharide. The β-barrel is sealed at the extracellular side, but molecular dynamic simulations suggest that the short loop Plug-S is sufficiently flexible to open a tunnel for the exopolysaccharide transport. This gating model is corroborated by single-channel conductivity measurements, where a deletion of Plug-S renders a constitutively open β-barrel. Our structural and functional analysis offers a comprehensive view on this pathogenicity-relevant complex and suggests the route taken by the exopolysaccharide at the final secretion step.
History
DepositionOct 28, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51916.png

Downloads & links

-
Map

FileDownload / File: emd_51916.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å		0.73 Å/pix.
x 360 pix.
= 261.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.47410968 - 1.0162237
Average (Standard dev.)-0.0008344693 (±0.039134275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_51916_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51916_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Exopolysaccharide transporter PelBC

EntireName: Exopolysaccharide transporter PelBC
Components
  • Complex: Exopolysaccharide transporter PelBC
    • Protein or peptide: PelB
    • Protein or peptide: PelC
  • Ligand: PHOSPHATIDYLETHANOLAMINE

-
Supramolecule #1: Exopolysaccharide transporter PelBC

SupramoleculeName: Exopolysaccharide transporter PelBC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

-
Macromolecule #1: PelB

MacromoleculeName: PelB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 135.273703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANSSAADKH PQARLLNPWA LLPVALGVAL VLWLTFNSEE VFMPSGDGEP DAVSVNYAEL LLQAHPENDA LRLTLIDLLV KLGDFEQAR HHLARLRGKD RLATPFYEVE LDILGALARP EGMDEEQTRR LLERLRKIEH VSLNDAMLER LARHALALDA P DLAARTFA ...String:
MANSSAADKH PQARLLNPWA LLPVALGVAL VLWLTFNSEE VFMPSGDGEP DAVSVNYAEL LLQAHPENDA LRLTLIDLLV KLGDFEQAR HHLARLRGKD RLATPFYEVE LDILGALARP EGMDEEQTRR LLERLRKIEH VSLNDAMLER LARHALALDA P DLAARTFA ELAGRDPQGR QRWLDEAARW YLASGEPLPA ADIQRQLAEA QTEPAKRLAY LRQAFASLLA GERGEQAALL LD ERLDALP EDESTLAWLA QGVRAAEGSQ RYDLAERFIR RWRELRPEDH EALAADLRLN MAAGRVERAW EVGQELLALR PED RTLLAD LARLGEWTGN GPRALGFWKQ LLAGADDPAL REHAWRLSLQ MFDFDSAIEL LAPIGAQRQM TDEELDALVY SHET RGTPE EGEAWLRGYV QRYPKQRLAW QRLQQILEHT QQLQEETGVW ARMARHFPLS VKERMQWAET HWNLFDPRQA WKVLA GVDT RAIREPEFWR LRAALAWALE QDDDARAAYE RMLALDIRLN SRDEDQLIAL YRDSNPKQAL QVLIGSWQRS RDPRRL ASA LQLAENLHDW PALKSLLAEA EGLPEAQGSP YYWVARARLA EQEGHGDVAE RLYREALVRF PGENLVRERL LWFYIDR GR RDSLAPLLAQ WHGLALRDST LWLPFASASL LLERNDQALA WFRLYLKSNP NDWLVQAAYA DALDASGYQD KALRLRRL L LRRLDREAVR ATPDSFATYL RLLAVAQGPL LAQGEARRAW NGEPAMLQLW FEQFLDQLAA TNQEPLKDNW LAWARGRGL KIGRNEEIQA ALRSQNRAAL QRLLERGELD PAQRVEALVR LGHGGEALGE ALGALGDGHS RDNREQLRRQ AAEILERTPQ GLQLGWNKR DFGGLDFKGP TLRAARHLGD DWYADLELGS GRYHGDALDS SLLGSERNAR LTLRRELADG FAAATLDGSW R DDEDRHGL GVLRNWRLSS RDELEAGLDW HRETDETGLM RALGMRDSLR LGGRHTLSGR DQLSWSLAHN RFSTRQGDDL GN GEALSLE WAHTLFFDGP AWQLRGGIDY QRNRLENRVP DDLLAAHGGA LALDGARSQD LLQDRYGQVY LGSTWRRGFP GAL NRSRPQ YTWIVDTLAG WQWTEKEFNY GIDLGIGMEL LGDDELAFTF GYQSAPQGGG GDAGGTLGVT YSTRFGR

UniProtKB: PelB

-
Macromolecule #2: PelC

MacromoleculeName: PelC / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 18.693111 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQSIRCLALA AVALFMAGCS SFTSESATPL ARGAQWGLVP LLNYSQAPQA GERAEQILLS VLAEEGVRPR LYPAQPQGDL QLVDDRERQ QRALDWARQQ KLAYVVTGSV EEWQYKNGLD GEPAVGVSLQ VLEPASGRVL WSTSGARAGW SRESLAGAAQ K VLRELVGD LRLE

UniProtKB: PelC

-
Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 27 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123975
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more